Research workbench
The crystal structure of protease SAPP1P from candida parapsilosis in complex with the HIV protease inhibitor ritonavir
Analyse The crystal structure of protease SAPP1P from candida parapsilosis in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TNE
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted aspartic protease
- EC
- 3.4.23.24
- UniProt
- B8YPM3
- Ligands
- RIT
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Secreted aspartic protease (EC 3.4.23.24) | protein | 339 | 9% helix, 45% strand | B8YPM3 |
Ligands and binding sites
- RIT · Ritonavir · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.70 | 0.76 | 78 | RIT |
| 2 | 826 | 0.70 | 0.76 | 66 | RIT |
Interfaces
1 interface between chains.
- A–B · 1355 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3TNE · The crystal structure of protease Sapp1p from Candida parapsilosis in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B8YPM3
- Elsewhere: RCSB PDB 3TNE · PDBe 3TNE · UniProt B8YPM3
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